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Bioinformatics Advance Access published online on April 8, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp241
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms

Triinu Koressaar 1, Kai Jõers 2 and Maido Remm 1

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010, Estonia 1
Quattromed HTI® Laborid, Nooruse 9, Tartu 50411, Estonia 2

*To whom correspondence should be addressed. Dr. Triinu Koressaar, E-mail: triinu_k{at}ut.ee


  Abstract

Motivation. The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.

Results. We have developed a novel computational method that identifies species-specific repeats from microbial organisms and automatically designs species-specific PCR primers for these repeats. We tested the methodology on 30 randomly chosen microbial species and we demonstrate that species-specific repeats longer than 300 bp exist in all these genomes. We also used our methodology to design species-specific PCR primers for 86 repeats from 5 medically relevant microbial species. These PCR primers were tested experimentally. We demonstrate that using species-specific repeats as a PCR template region can increase the sensitivity of PCR in diagnostic tests.

Availability and Implementation. A web version of the method called MultiMPrimer3 was implemented and is freely available at http://bioinfo.ut.ee/multimprimer3/.

Contact: maido.remm{at}ut.ee

Associate Editor: Dr. Alex Bateman

Received on January 16, 2009; revised on March 16, 2009; accepted on April 3, 2009

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